Variant report

Variant	rs56397887
Chromosome Location	chr3:179758349-179758350
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:61)
Chromatin interactive
region (count:0)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr3:179758307-179758357	CMK	blood:	n/a
2	chr3:179758307-179758357	GM12878	blood:	n/a
3	chr3:179758307-179758357	HCF	heart:	n/a
4	chr3:179758307-179758357	HEK293	kidney:	embryo
5	chr3:179758307-179758357	K562	blood:	n/a
6	chr3:179758307-179758357	ProgFib	skin:	n/a
7	chr3:179758307-179758357	MCF10A-Er-Src	breast:	n/a
8	chr3:179758307-179758357	SK-N-MC	brain:	n/a
9	chr3:179758307-179758357	AG09309	skin:	n/a
10	chr3:179758307-179758357	HL-60	blood:	n/a
11	chr3:179758307-179758357	GM06990	blood:	n/a
12	chr3:179758307-179758357	Hela-S3	cervix:	n/a
13	chr3:179758307-179758357	AG09319	gingival:	n/a
14	chr3:179758307-179758357	Hepatocyte	liver:	n/a
15	chr3:179758307-179758357	HPAEpiC	pulmonary alveolar:	n/a
16	chr3:179758307-179758357	NHBE	bronchial:	n/a
17	chr3:179758307-179758357	IMR90	lung:	fetal
18	chr3:179758307-179758357	GM12892	blood:	n/a
19	chr3:179758307-179758357	GM19239	blood:	n/a
20	chr3:179758307-179758357	H1-hESC	embryonic stem cell:	embryo
21	chr3:179758307-179758357	HMEC	breast:	n/a
22	chr3:179758307-179758357	NT2-D1	testis:	n/a
23	chr3:179758307-179758357	HIPEpiC	eye:	n/a
24	chr3:179758307-179758357	ECC-1	luminal epithelium:	n/a
25	chr3:179758307-179758357	HRCEpiC	kidney:	n/a
26	chr3:179758307-179758357	HAEpiC	amniotic membrane:	n/a
27	chr3:179758307-179758357	U87	brain:	n/a
28	chr3:179758307-179758357	HUVEC	blood vessel:	n/a
29	chr3:179758307-179758357	HepG2	liver:	n/a
30	chr3:179758307-179758357	NB4	blood:	n/a
31	chr3:179758307-179758357	PrEC	prostate:	n/a
32	chr3:179758307-179758357	AG10803	skin:	n/a
33	chr3:179758307-179758357	AG04449	skin:	fetal
34	chr3:179758307-179758357	RPTEC	kidney:	n/a
35	chr3:179758307-179758357	ovcar-3	ovarian:	n/a
36	chr3:179758307-179758357	MCF-7	breast:	n/a
37	chr3:179758307-179758357	PANC-1	pancreas:	n/a
38	chr3:179758307-179758357	HCM	heart:	n/a
39	chr3:179758307-179758357	A549	lung:	n/a
40	chr3:179758307-179758357	HEEpiC	esophagus:	n/a
41	chr3:179758307-179758357	HNPCEpiC	eye:	n/a
42	chr3:179758307-179758357	NH-A	brain:	n/a
43	chr3:179758307-179758357	HCPEpiC	choroid plexus:	n/a
44	chr3:179758307-179758357	SK-N-SH	brain:	n/a
45	chr3:179758307-179758357	HCT-116	colon:	n/a
46	chr3:179758307-179758357	LNCaP	prostate:	n/a
47	chr3:179758307-179758357	PFSK-1	brain:	n/a
48	chr3:179758307-179758357	AG04450	lung:	fetal
49	chr3:179758307-179758357	GM12891	blood:	n/a
50	chr3:179758307-179758357	T-47D	breast:	n/a

No data

Variant related genes	Relation type
PEX5L	CpG island

Extended variants
information (count: 42 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs11713683	0.80[ASN][1000 genomes]
rs13324196	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13325101	0.84[ASN][1000 genomes]
rs13325206	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1522115	0.80[ASN][1000 genomes]
rs1529269	0.83[ASN][1000 genomes]
rs1851352	0.85[ASN][1000 genomes]
rs1851353	0.85[ASN][1000 genomes]
rs2204095	0.85[ASN][1000 genomes]
rs57729381	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs59205301	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs61623675	0.98[ASN][1000 genomes]
rs6443685	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6443687	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6443688	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6787707	0.82[AMR][1000 genomes]
rs6788776	0.84[ASN][1000 genomes]
rs6797922	0.82[ASN][1000 genomes]
rs6800148	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs73883446	0.80[AMR][1000 genomes]
rs73883462	0.80[ASN][1000 genomes]
rs73883468	0.80[ASN][1000 genomes]
rs73883469	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs73883479	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73883495	0.83[ASN][1000 genomes]
rs7615924	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7630527	0.80[ASN][1000 genomes]
rs7640838	0.85[ASN][1000 genomes]
rs939824	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs939825	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs940522	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9809603	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9823631	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9826864	0.84[ASN][1000 genomes]
rs9828423	0.83[ASN][1000 genomes]
rs9828621	0.94[ASN][1000 genomes]
rs9833738	0.98[ASN][1000 genomes]
rs9866193	0.83[ASN][1000 genomes]
rs9870941	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9881655	0.80[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv534210	chr3:179666123-179899347	Enhancers Bivalent Enhancer Genic enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv1000756	chr3:179672703-179827373	Enhancers Active TSS Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:179755400-179758400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr3:179755400-179758600	Weak transcription	HMEC	breast
3	chr3:179758200-179759600	Enhancers	Muscle Satellite Cultured Cells	--

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